8RHB: Microtubule-associated kinesin-1 tail complex

Microtubule-associated kinesin-1 tail complex bound to AMPPNP, single-headed state. Determined by electron microscopy at 3.0 Å resolution. Released 20 Nov 2024.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Sus scrofa, Homo sapiens
Chains: 5
Atoms: 9,539
Mol. weight: 322.88 kDa
Ligands: GTP, MG, ANP, TA1
Released: 20 Nov 2024

Explore 8RHB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RHB contains 57 α-helices and 56 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 23 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	12
α-helix	10-27	18
β-strand	53-55	3	13
β-strand	61-63	3	13
β-strand	65-69	5	12
α-helix	72-80	9
β-strand	93-94	2	12
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-127	13
β-strand	131-138	8	12
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-171	7	12
α-helix	172-174	3
α-helix	183-193	11
β-strand	200-204	5	12
α-helix	206-215	10
α-helix	224-243	20
α-helix	252-259	8
β-strand	269-273	5	12
α-helix	279-281	3
α-helix	288-295	8
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-321	10	12
α-helix	325-337	13
β-strand	343	1	12
β-strand	351-356	6	12
α-helix	359-361	3
β-strand	373-381	9	12
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	415-436	22

Chain B: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10-28	19
β-strand	30	1	2
β-strand	36	1	2
α-helix	41-47	5
β-strand	65-69	5	1
α-helix	73-80	8
β-strand	93-94	2	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	112-127	16
β-strand	132-140	9	1
α-helix	145-160	16
β-strand	165-171	7	1
α-helix	172-174	3
α-helix	183-197	15
β-strand	200-204	5	1
α-helix	206-215	10
α-helix	224-238	15
β-strand	248	1	3
α-helix	252-259	8
β-strand	267-268	2	1
β-strand	269-273	5	3
α-helix	288-295	8
β-strand	312-321	10	3
α-helix	325-338	14
β-strand	343	1	3
β-strand	351-356	6	3
α-helix	359-360	2
β-strand	373-381	9	3
α-helix	382-384	3
α-helix	385-400	16
α-helix	406-409	4
α-helix	415-434	20

Chain K: 15 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	4
β-strand	10-15	6	5
α-helix	16-19	4
α-helix	20-23	4
β-strand	29	1	6
β-strand	32-34	3	7
β-strand	38-40	3	7
β-strand	45-47	3	7
β-strand	50-52	3	5
α-helix	58-65	8
α-helix	67-75	9
β-strand	79-85	7	5
β-strand	86	1	8
α-helix	91-95	5
β-strand	97	1	9
β-strand	105	1	9
α-helix	107-121	15
β-strand	126-137	12	5
β-strand	142-144	3	5
β-strand	154-157	4	10
β-strand	163-166	4	10
β-strand	171-173	3	5
α-helix	176-188	13
β-strand	192-193	2	11
β-strand	201-202	2	11
β-strand	206-216	11	5
β-strand	222-223	2	5
β-strand	226-231	6	5
α-helix	232-234	3
β-strand	235	1	8
α-helix	238-241	4
α-helix	246-270	25
α-helix	277-279	3
α-helix	281-285	5
α-helix	287-291	5
β-strand	295-302	8	5
β-strand	305	1	6
α-helix	306-308	3
α-helix	309-323	15
β-strand	326-328	3	4
β-strand	333	1	5

Chain t: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	922-925	4	5

Chain T: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	919-922	4	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin beta chain	B	protein	445	Sus scrofa	P02554 (AlphaFold model)
Kinesin-1 heavy chain	K, T	protein	963	Homo sapiens	P33176 (AlphaFold model)
Tubulin alpha-1B chain	A	protein	451	Sus scrofa	Q2XVP4 (AlphaFold model)
Kif5b Tail	t	protein	6	Homo sapiens	P33176 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8RHB_1 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Sequence of entity 2 (K, T), FASTA

>8RHB_2 Kinesin-1 heavy chain (chains K, T)
MADLAECNIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIASKPYAFDRVFQSSTSQEQ
VYNDCAKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEGKLHDPEGMGIIPRIVQDIFNYIY
SMDENLEFHIKVSYFEIYLDKIRDLLDVSKTNLSVHEDKNRVPYVKGCTERFVCSPDEVM
DTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSK
TGAEGAVLDEAKNINKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNCRTTIVI
CCSPSSYNESETKSTLLFGQRAKTIKNTVCVNVELTAEQWKKKYEKEKEKNKILRNTIQW
LENELNRWRNGETVPIDEQFDKEKANLEAFTVDKDITLTNDKPATAIGVIGNFTDAERRK
CEEEIAKLYKQLDDKDEEINQQSQLVEKLKTQMLDQEELLASTRRDQDNMQAELNRLQAE
NDASKEEVKEVLQALEELAVNYDQKSQEVEDKTKEYELLSDELNQKSATLASIDAELQKL
KEMTNHQKKRAAEMMASLLKDLAEIGIAVGNNDVKQPEGTGMIDEEFTVARLYISKMKSE
VKTMVKRCKQLESTQTESNKKMEENEKELAACQLRISQHEAKIKSLTEYLQNVEQKKRQL
EESVDALSEELVQLRAQEKVHEMEKEHLNKVQTANEVKQAVEQQIQSHRETHQKQISSLR
DEVEAKAKLITDLQDQNQKMMLEQERLRVEHEKLKATDQEKSRKLHELTVMQDRREQARQ
DLKGLEETVAKELQTLHNLRKLFVQDLATRVKKSAEIDSDDTGGSAAQKQKISFLENNLE
QLTKVHKQLVRDNADLRCELPKLEKRLRATAERVKALESALKEAKENASRDRKRYQQEVD
RIKEAVRSKNMARRGHSAQIAKPIRPGQHPAASPTHPSAIRGGGAFVQNSQPVAVRGGGG
KQV

Sequence of entity 3 (A), FASTA

>8RHB_3 Tubulin alpha-1B chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 4 (t), FASTA

>8RHB_4 Kif5b Tail (chains t)
AKPIRP

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1
TA1	Taxol	C47 H51 N O14	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

Primary citation

Microtubule association induces a Mg-free apo-like ADP pre-release conformation in kinesin-1 that is unaffected by its autoinhibitory tail. Atherton, J., Chegkazi, M.S., Leusciatti, M. et al. Nat Commun (2025) 16:6214-6214. DOI 10.1038/s41467-025-61498-3 · PubMed

Other PDB entries of the same protein (UniProt P02554 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9U6A 1.92 Å, Tubulin-DARPin D1 in complex with a flavone
7TTF 2.1 Å, Tubulin-RB3_SLD in complex with compound 12k
7L05 2.21 Å, Complex of novel maytansinoid M24 bound to T2R-TTL (two tubulin alpha/beta heterodimers,…
5JQG 2.24 Å, An apo tubulin-RB-TTL complex structure used for side-by-side comparison
5XKH 2.25 Å, Crystal structure of T2R-TTL-CF1 complex
7TTD 2.27 Å, Tubulin-RB3_SLD in complex with compound 12e
5XP3 2.3 Å, Crystal structure of apo T2R-TTL
6XES 2.32 Å, Tubulin-RB3_SLD in complex with compound 40a
7EMJ 2.33 Å, Crystal structure of T2R-TTL-Barbigerone complex
7XQY 2.35 Å, Crystal structure of T2R-TTL-15 complex
7EXC 2.39 Å, Crystal structure of T2R-TTL-1129A2 complex
6LS4 2.4 Å, A novel anti-tumor agent S-40 in complex with tubulin

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